We studied the systematic status of a form of Pollimyrus of the lower Kwando River that is flanked by the Okavango River, inhabited by Pollimyrus castelnaui (Boulenger, 1911), and the Zambezi River, inhabited by Pollimyrus marianne Kramer et al., 2003. In morphology and electric organ discharges (EODs), the Kwando phenotype proved well differentiated from both P. castelnaui andP. marianne. Sequence analysis of the cyt b gene confirmed that the three forms or species form a monophyletic clade, with P. castelnaui sister to the other two species. Genomic fingerprinting with ISSR-PCR confirmed differentiation of the Kwando form, that we recognize as a different species,P. cuandoensis sp. nov., from its sister species, P. marianne. A considerable amount of EOD and morphological variation was revealed among samples of P. cuandoensis sp. nov. from four different locations on the lower Kwando River, possibly due to hybrid introgression. This seems an ideal system for testing theories of parapatric speciation.